SLTM

SAFB like transcription modulator, the group of RNA binding motif containing

Basic information

Region (hg38): 15:58879049-58933679

Links

ENSG00000137776 ∙ NCBI:79811 ∙ ∙ HGNC:20709 ∙ Uniprot:Q9NWH9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLTM gene.

• Inborn genetic diseases (28 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLTM gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	0	0

Variants in SLTM

This is a list of pathogenic ClinVar variants found in the SLTM region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-58883674-C-T		not specified	Uncertain significance (Sep 14, 2023)
15-58883692-C-G		not specified	Uncertain significance (Mar 01, 2023)
15-58883759-C-G		not specified	Uncertain significance (Dec 06, 2023)
15-58887040-C-T		not specified	Uncertain significance (Sep 26, 2022)
15-58887061-G-C		not specified	Uncertain significance (Aug 17, 2022)
15-58887063-G-A		not specified	Uncertain significance (Feb 09, 2023)
15-58887236-G-A		not specified	Uncertain significance (Mar 20, 2023)
15-58887250-A-G		not specified	Uncertain significance (Oct 05, 2023)
15-58887278-G-T		not specified	Uncertain significance (Jul 14, 2021)
15-58887289-T-C		not specified	Uncertain significance (Nov 08, 2022)
15-58887316-G-T		Jeune thoracic dystrophy	Likely pathogenic (-)
15-58887323-T-G		not specified	Uncertain significance (Jan 08, 2024)
15-58887338-C-G		not specified	Uncertain significance (Jan 30, 2024)
15-58887358-C-T		not specified	Uncertain significance (Jun 18, 2021)
15-58887376-C-T		not specified	Uncertain significance (Jan 16, 2024)
15-58887478-T-C		not specified	Uncertain significance (Jan 09, 2024)
15-58888454-T-C		not specified	Uncertain significance (Jan 09, 2024)
15-58888490-T-C		not specified	Uncertain significance (May 24, 2023)
15-58888520-A-G		not specified	Uncertain significance (Jun 29, 2023)
15-58889511-T-G		not specified	Uncertain significance (Nov 04, 2023)
15-58890363-C-A		not specified	Uncertain significance (Dec 22, 2023)
15-58890366-T-G		not specified	Uncertain significance (Jun 06, 2023)
15-58890385-G-A		not specified	Uncertain significance (Jan 04, 2024)
15-58890403-C-T		not specified	Uncertain significance (Jan 04, 2022)
15-58893841-C-A		not specified	Uncertain significance (Apr 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLTM	protein_coding	protein_coding	ENST00000380516	21	54609

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00215	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.53	416	588	0.707	0.0000340	6798
Missense in Polyphen		82	116.14	0.70602		1146
Synonymous	0.137	197	199	0.988	0.0000110	1921
Loss of Function	6.30	11	66.5	0.165	0.00000471	693

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000264	0.000264
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000533	0.0000527
Middle Eastern	0.000273	0.000272
South Asian	0.0000338	0.0000327
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: When overexpressed, acts as a general inhibitor of transcription that eventually leads to apoptosis. {ECO:0000250}.

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.267
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.77

Haploinsufficiency Scores

• pHI: 0.769
• hipred: Y
• hipred_score: 0.575
• ghis: 0.669

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.952

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sltm

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;apoptotic process;regulation of mRNA processing
• Cellular component: nucleus;nucleoplasm;nuclear body
• Molecular function: RNA binding;sequence-specific DNA binding